...or just substitute the missing EPO with "MERP-Tidak Kembali". It's basically EPO for people who already left Indonesia. Your former university seems to be helpful and showing responsibility, so this will be the best and easiest way. As a sponsor they will arrange this locally. They might need proof of your departure to process it (i.e. copy of departure stamp or flight tickets) besides the other immigration docs related to your KITAS as part of the procedure. I guess the details depend on the local immigration office and they will advise. Attached is what the MERP looks like, you should ask them for a copy.
It's an easy procedure. Going out/emigration is always easy, coming in/immigration much harder,
I think it applies to all countries.